An influential watchdog will today question the value of the government's £45bn programme to replace or refurbish all 3,400 secondary schools in England by 2020. MPs on the education select committee will suggest that some of the cash might be better directed to making buildings more environmentally sustainable by reducing carbon emissions or boosting pre-school learning. An increase in university research budgets should also be considered.

The report on the early stages of the Building Schools for the Future (BSF) programme, comparable to Victorian and post-second world war school building, does not say the programme is a waste of money nor recommend a halt, but says the scheme must be regularly reviewed.

It questions the use of the public finance initiative (PFI) for about half the package - the funding method by which private companies pay to take part and then lease buildings back to schools on long contracts, often 25-30 years.

The MPs also want local authorities to have more freedom over the regeneration of schools - there have been complaints that the government forces them into agreeing to semi-independent academies as part of BSF.

The programme has been hit by delays but the first new mainstream school buildings under its banner will open in Bristol next month, with about a dozen projects completed by next April. About 50 more are expected the following year.

The MPs said other building programmes over the past 10 years had addressed a backlog of leaky, dilapidated buildings and asked whether £45bn was "too much" to be spent on buildings.

"BSF has begun by providing resources to areas with low levels of educational attainment. Once those areas ... have their projects in place, it could be argued that investment to replace buildings becomes less of a priority. That might be the point at which BSF could be drawn to a close and a different approach to capital and other investment in schools could be adopted."

While the programme represented "an unprecedented opportunity" to transform education, there was "a danger that everyone involved will concentrate on getting through to the end and that the question of whether the project's scope and aims remain appropriate will not be asked."

Three PFI-funded schools not in the BSF programme have already closed or are closing, leaving authorities with big bills, and the committee was worried that shifts in pupil populations could lead to more costly closures.

Children's minister Kevin Brennan said BSF was "a once-in-a-generation opportunity to address the historic legacy of under-investment in secondary schools". It would equip schools "to inspire young minds and support teachers", make the most of new technology and provide flexible accommodation to respond to changes in educational practice.